JSmol in Moodle

Steven Ford (Developer)

Research output: Non-textual formSoftware


When I studied undergrad chemistry at Glasgow we needed to buy textbooks and a simple 'Orbit' molecular models kit (they're still for sale too!). It was a simple, but useful, way of picturing what was happening in chemical reactions at an atomic level. I really wanted to try and get an online system for allowing students to 'interact' with molecules and help them understand the 3 dimensional thinking that required for topic like stereochemistry.

I’d played around with various ideas until I settled on using Jmol and JSmol. These use javascript and/or http 5 to produce chemical structures that users can interact with. There seemed to be lots of (what is for me) complicated code online, but then I came across some documentation that linked to some simple instructions that gave me a lead. (See note 1)

I really wanted to embed the interactive images into our online learning website (we call it myplace: it’s a customised version of moodle). However, myplace doesn’t allow scripts to run, or embedded iframes of the type I wanted to use. (WordPress, this blogging site, also has similar restrictions.) I’d played around with the idea of writing the javascript into my own uni webpages, and striping the required display parameters out of the refering URL – but my javascript just isn’t good enough! I went back to using anchors, href and src tags in iframes and embedded weblinks (which display automatically below the weblink) but I couldn’t get anything to work, Eventually I settled on the 'in pop-up' webpage resource.
Original languageEnglish
Place of Publication[S.I.]
Media of outputOnline
Publication statusPublished - 9 Jul 2021


  • JSmol
  • Jmol
  • moodle
  • myplace
  • protein structure


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